├── INSTALL ├── README.md ├── circularRNApipeline_Cluster ├── README ├── analysis │ ├── align.sh │ ├── combineSwappedReadsGLM.py │ ├── combineSwappedReadsGLM.sh │ ├── combineSwappedReadsNaive.py │ ├── combineSwappedReadsNaive.sh │ ├── createSwappedDirectories.py │ ├── createSwappedDirectories.sh │ ├── filterFDR.py │ ├── filterFDR.sh │ ├── parseForAnalysis.sh │ ├── predictJunctions.sh │ ├── predictJunctions_tableData.r │ ├── preprocessAlignedReads.sh │ ├── utils_juncReads_minimal.py │ ├── utils_os.py │ └── writeTaskIdFiles.py ├── denovo_scripts │ ├── README │ ├── align_unaligned_in_pieces_step2.pl │ ├── denovo_scripts.batch │ ├── depends_denovo.sh │ ├── process_directory_unaligned.pl │ ├── process_max_denovo.pl │ ├── process_representatives_for_lindas_pipeline.pl │ ├── retreive_represent.pl │ ├── stat_read_matchup_3a.pl │ └── test_stats_step2_3c.pl ├── depends.sh ├── findCircularRNA_SGE.sh ├── findCircularRNA_SLURM.sh ├── qualityStats │ ├── ParseFastQ.py │ ├── getUnalignedReadCount.py │ ├── qualityStatsCat.sh │ └── qualityStatsSingleSample.sh └── sampleInfo.sh ├── circularRNApipeline_Standalone ├── ParseFastQ.py ├── README ├── analysis │ ├── align.sh │ ├── combineSwappedReadsGLM.py │ ├── combineSwappedReadsNaive.py │ ├── createSwappedDirectories.py │ ├── filterFDR.py │ ├── filterFDR.sh │ ├── parseForAnalysis.sh │ ├── predictJunctions.sh │ ├── predictJunctions_tableData.r │ ├── preprocessAlignedReads.sh │ ├── utils_juncReads_minimal.py │ ├── utils_os.py │ └── writeTaskIdFiles.py ├── completeRun.sh ├── denovo_scripts │ ├── README │ ├── align_unaligned_in_pieces_step2.pl │ ├── process_directory_unaligned.pl │ ├── process_max_denovo.pl │ ├── process_representatives_for_lindas_pipeline.pl │ ├── retreive_represent.pl │ ├── stat_read_matchup_3a.pl │ └── test_stats_step2_3c.pl ├── findCircularRNA.sh └── qualityStats │ ├── ParseFastQ.py │ ├── getUnalignedReadCount.py │ ├── qualityStatsAll.sh │ ├── qualityStatsCat.sh │ └── qualityStatsSingleSample.sh ├── createJunctionIndex ├── 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